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Keep in mind that the stuff can and will be customized other way than Theme Designer. The worst offender I think the #WikiHeader element. One of the most common mods to it is adding a background... but the element doesn't span full width of the page and margins change with breakpoints. It requires that much code to make it span full width to go with a single line adding a background. And one could've make it in a way that takes into account the fact that people add background there.

#WikiaArticle with overflow: hidden. I get why it's there.. to prevent adding stuff with position:fixed that can obscure UI and ads... but again it doesn't take into account simple css like adding shadows to elements in the content area. Like infoboxes or navboxes. Shadows get cut off at the edge of the article and an average user that found the code for shadows have no idea how to deal with it. Why not add some padding to it, or have overflow:hidden on the page element and make the content have lower z-index then rest of the UI.

There is a built-in function called {{GRAMMAR:form|noun}}, I imagine it's not much of use for English speakers but it could come is handy for langs that have very different for some words... like Polish. And it works as it should right of the bat... but the problem is with updating the list. Normally it requires putting forms in the $wgGrammarForms variable, but on Wikia you need someone with WikiFactory access for this, and that makes it a hassle. I think it could be adapted into the form of a multi level list MediaWiki message

There are a lot of scripts that add their entry points to the toolbar. PortableCSSPad, BatchDelete, Mass Null Edit to name a few. But since the release of Global Shortcuts I found myself only using the toolbar to access these features... the dot-search is very convenient but it can only be used to access built-in stuff. If there was a way to add custom entries to the search it could potentially (at least for me) remove the need to have the toolbar on hand. Function to add this stuff could take a label for the entry and either a string with url to the page or a callback function called when user selects the entry.